1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.DistanceModelI;
4 import jalview.io.DataSourceType;
5 import jalview.io.FileParse;
6 import jalview.io.ScoreMatrixFile;
8 import java.io.IOException;
9 import java.util.LinkedHashMap;
13 * A class that can register and serve instances of ScoreModelI
15 public class ScoreModels
17 private final ScoreMatrix BLOSUM62;
19 private final ScoreMatrix PAM250;
21 private final ScoreMatrix DNA;
23 private static ScoreModels instance = new ScoreModels();
25 private Map<String, DistanceModelI> models;
27 public static ScoreModels getInstance()
33 * Private constructor to enforce use of singleton. Registers Jalview's
34 * "built-in" score models:
38 * <li>SeqSpace (identity matrix)</li>
40 * <li>Sequence Feature Similarity</li>
41 * <li>Percentage Identity</li>
47 * using LinkedHashMap keeps models ordered as added
49 models = new LinkedHashMap<String, DistanceModelI>();
50 BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
51 PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
52 loadScoreMatrix("scoreModel/seqspace.scm");
53 // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
54 // registerScoreModel(new IdentityScoreModel());
55 DNA = loadScoreMatrix("scoreModel/dna.scm");
56 registerScoreModel(new FeatureDistanceModel());
57 registerScoreModel(new PIDDistanceModel());
61 * Tries to load a score matrix from the given resource file, and if
62 * successful, registers it.
67 ScoreMatrix loadScoreMatrix(String resourcePath)
72 * delegate parsing to ScoreMatrixFile
74 FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
75 ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
76 registerScoreModel(sm);
78 } catch (IOException e)
80 System.err.println("Error reading " + resourcePath + ": "
87 * Registers a pairwise score model
91 public void registerScoreModel(PairwiseScoreModelI sm)
93 registerScoreModel(new PairwiseDistanceModel(sm));
97 * Answers an iterable set of the registered score models. Currently these are
98 * returned in the order in which they were registered.
102 public Iterable<DistanceModelI> getModels()
104 return models.values();
107 public DistanceModelI forName(String s)
109 return models.get(s);
112 public void registerScoreModel(DistanceModelI sm)
114 DistanceModelI sm2 = models.get(sm.getName());
117 System.err.println("Warning: replacing score model " + sm2.getName());
119 models.put(sm.getName(), sm);
123 * Returns the default peptide or nucleotide score model, currently BLOSUM62
129 public ScoreMatrix getDefaultModel(boolean forPeptide)
131 return forPeptide ? BLOSUM62 : DNA;
134 public ScoreMatrix getBlosum62()
139 public ScoreMatrix getPam250()